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115,814 results • Page
1 of 2317
Sort: Views
Rank
Views
Votes
Replies
65
votes
3
replies
292k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 12 months ago by
Ram
43k • written 9.8 years ago by
Whoknows
▴ 960
226
votes
39
replies
287k
views
33 follow
Gene Id Conversion Tool
david
updated 5 months ago by
Ram
43k • written 14.4 years ago by
Renee
▴ 620
279
votes
29
replies
280k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 16 months ago by
Ram
43k • written 11.4 years ago by
sohadb1357
▴ 640
331
votes
92
replies
237k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 7 months ago by
kalavattam
▴ 190 • written 13.1 years ago by
Biomed
4.9k
43
votes
24
replies
205k
views
25 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 23 months ago by
matthew.pace
▴ 60 • written 10.3 years ago by
Arpitha Hebbar
▴ 210
12
votes
6
replies
198k
views
How can I uninstall my packages in Rstudio
R
Bioconductor
updated 3.5 years ago by
zx8754
11k • written 6.1 years ago by
hassanlou110
▴ 40
119
votes
31
replies
197k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 4 months ago by
Ram
43k • written 13.9 years ago by
Eric Normandeau
11k
62
votes
14
replies
194k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 10 months ago by
zx8754
11k • written 11.1 years ago by
Diana
▴ 910
130
votes
19
replies
182k
views
13 follow
What'S The Difference Between Cds And Orf?
cds
orf
updated 2.9 years ago by
kajumi
• 0 • written 11.8 years ago by
shiy05
▴ 360
287
votes
39
replies
182k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 12 months ago by
Ram
43k • written 9.6 years ago by
Obi Griffith
20k
151
votes
42
replies
180k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 22 months ago by
Ram
43k • written 12.0 years ago by
Obi Griffith
20k
205
votes
21
replies
178k
views
12 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 16 months ago by
Istvan Albert
100k • written 13.4 years ago by
Andrea_Bio
★ 2.8k
163
votes
8
replies
177k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 20 months ago by
Ram
43k • written 11.3 years ago by
lyz10302012
▴ 450
124
votes
13
replies
172k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 6 months ago by
Ram
43k • written 13.7 years ago by
Biomed
4.9k
135
votes
18
replies
169k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 15 months ago by
katieostrouchov
▴ 30 • written 10.3 years ago by
timjoncooper
▴ 320
142
votes
14
replies
169k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Pierre Lindenbaum
160k
98
votes
39
replies
154k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 11 months ago by
Dan
▴ 180 • written 11.7 years ago by
abi
▴ 390
231
votes
38
replies
145k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 9 months ago by
Ram
43k • written 11.1 years ago by
Malachi Griffith
19k
361
votes
81
replies
143k
views
34 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
11 months ago by
ole.tange
★ 4.4k
791
votes
167
replies
138k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.5k • written 7.3 years ago by
Istvan Albert
100k
147
votes
31
replies
136k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 7 months ago by
Ram
43k • written 12.1 years ago by
Anima Mundi
★ 2.9k
10
votes
4
replies
134k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r
programming
updated 12.7 years ago by
Stefano Berri
4.4k • written 12.7 years ago by
Don
▴ 20
13
votes
8
replies
129k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 17 months ago by
Ram
43k • written 12.4 years ago by
Zhshqzyc
▴ 520
129
votes
32
replies
129k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 23 months ago by
Ram
43k • written 13.0 years ago by
Gon
▴ 540
68
votes
18
replies
127k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing
samtools
updated 7 weeks ago by
Pierre Lindenbaum
160k • written 9.4 years ago by
Kizuna
▴ 870
166
votes
52
replies
127k
views
28 follow
Fastq Convert To Fasta
perl
10.4 years ago by
biolab
★ 1.4k
23
votes
9
replies
126k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 13 months ago by
Ram
43k • written 8.9 years ago by
juan.rosas1
▴ 70
100
votes
9
replies
126k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 23 months ago by
henry-keen
▴ 40 • written 10.5 years ago by
newDNASeqer
▴ 760
26
votes
10
replies
123k
views
Calculating P-Values From Z-Scores
statistics
r
updated 21 months ago by
Ram
43k • written 12.1 years ago by
Diana
▴ 910
119
votes
25
replies
122k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human
fasta
sequence
bwa
updated 7.1 years ago by
Hajk-Georg Drost
▴ 160 • written 13.7 years ago by
Biomed
4.9k
3
votes
3
replies
118k
views
Find mismatch in two columns in a data frame in R
R
updated 8.0 years ago by
dan.shea
▴ 10 • written 8.0 years ago by
dirranrak
▴ 20
76
votes
26
replies
118k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 3 months ago by
cschu181
★ 2.8k • written 8.9 years ago by
Chenglin
▴ 260
119
votes
7
replies
117k
views
Bam And Indexed Bam Files
bam
index
12.2 years ago by
Sahel
▴ 260
46
votes
10
replies
115k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 15 months ago by
Ram
43k • written 11.0 years ago by
biorepine
★ 1.5k
115
votes
21
replies
113k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python
perl
comparison
updated 12.0 years ago by
Aditya Joshi
▴ 30 • written 12.4 years ago by
Niek De Klein
★ 2.6k
103
votes
34
replies
112k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 9 weeks ago by
Ram
43k • written 11.8 years ago by
GPR
▴ 390
105
votes
16
replies
110k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 4 days ago by
xiaoleiusc
▴ 140 • written 11.8 years ago by
GouthamAtla
12k
66
votes
9
replies
108k
views
10 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression
RNA-Seq
updated 13 months ago by
Ram
43k • written 6.5 years ago by
Renesh
★ 2.2k
91
votes
10
replies
107k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein
genes
pathway
analysis
function
updated 11.9 years ago by
Guangchuang Yu
★ 2.6k • written 11.9 years ago by
Wayne
★ 1.0k
296
votes
33
replies
106k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 12 months ago by
Ram
43k • written 10.4 years ago by
Obi Griffith
20k
28
votes
8
replies
106k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna
fpkm
rpkm
written 13.0 years ago by
User 5402
▴ 210
118
votes
15
replies
104k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 13.2 years ago by
Mona Mohamed
• 0 • written 13.4 years ago by
Terence
▴ 210
124
votes
56
replies
101k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 5 months ago by
William
▴ 30 • written 9.8 years ago by
kay
▴ 370
65
votes
10
replies
101k
views
6 follow
Fold change - a final explanation
RNA-Seq
updated 3.6 years ago by
naloy
▴ 10 • written 5.4 years ago by
Sebastian Hesse
▴ 340
31
votes
8
replies
97k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java
structure
algorithm
updated 13.2 years ago by
Hazel
• 0 • written 13.9 years ago by
Hazel
▴ 70
170
votes
41
replies
96k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 5 months ago by
Ram
43k • written 12.8 years ago by
Palu
▴ 250
85
votes
16
replies
95k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 16 months ago by
bhanu.chandra1
▴ 50 • written 8.9 years ago by
Prakki Rama
★ 2.7k
43
votes
8
replies
95k
views
samtools sorting and indexing
samtools
index
sort
updated 4.2 years ago by
onestop_data
▴ 330 • written 6.7 years ago by
ggman
▴ 80
238
votes
176
replies
94k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 9 months ago by
Ram
43k • written 8.6 years ago by
TriS
★ 4.7k
97
votes
19
replies
93k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc
fasta
sequence
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Giovanni M Dall'Olio
28k
115,814 results • Page
1 of 2317
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Answer: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential expression at pathway level
A: Difference between heatmap using Euclidian distance and Poisson distance
A: Difference between heatmap using Euclidian distance and Poisson distance
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Answer: Downloading epigenetic and mutation data of specific TCGA BRCA samples
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aUser
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Hi, you might have solve the problem, but for the future reference, I am writing this. The nomenclature of TCGA data set is explained here:…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Dora
▴ 10
Thank you so much for your reply! here is what I have after entering the command variableStep#chrom=NT_173277.1 Cavia porcellus strain…
Comment: Differential express genes in imbalance groups
by
Chris
▴ 260
Wow, the author of the tool reply. Thank you so much!
Comment: t-test in two groups, multiple rows
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It was my mistake. I converted the dataframe to matrix. It works! Thank you!
Comment: Differential express genes in imbalance groups
by
Gordon Smyth
★ 6.9k
I do mean the quality of each sample (as measured by residual variability in the linear model, in other words by consistency with other sam…
Comment: Differential express genes in imbalance groups
by
Chris Dean
▴ 390
That sounds super interesting. I have never heard of this approach before. When you say 'sample quality weights' are you referring to dif…
Answer: Beagle Phasing and Imputation
by
LChart
3.8k
Not doable with older versions of beagle. I seem to recall that it used to be recommended to re-code the sex chromosomes of males in the re…
Answer: Differential express genes in imbalance groups
by
Gordon Smyth
★ 6.9k
Imbalanced group sizes are no problem. Just analyse the data as it is. No need to throw data away! For a human study with a large number o…
Comment: Trim Galore: Automatic detection of adapters
by
Daniel
▴ 30
Got it, this clears things up. Thank you!
Answer: basal gene expression level
by
LChart
3.8k
I haven't seen any reliable way to estimate absolute RNA concentrations from sequencing data. Methods have been developed using [housekeepi…
Answer: Seurat 5 integration
by
jared.andrews07
★ 16k
You are still free to change whichever parameters you want for whichever method you're using. See `?IntegrateLayers` and whichever method y…
Answer: scRNAseq normalization
by
ATpoint
81k
It's perfectly fine to use log-transformation. The advantages of these more complicated methods usually depend on context and also on the w…
Answer: scRNAseq normalization
by
dsull
★ 5.6k
No, your log-transform might indeed be ok (or even better) for your analysis of interest. See https://www.nature.com/articles/s41592-023…
Answer: Transcription Start Site
by
el24
▴ 40
Here is a simple pythonic way to use biomart: import pybiomart as pbm dataset = pbm.Dataset(name='hsapiens_gene_ensembl', host="h…
Comment: data background noise
by
marco.barr
▴ 30
Thank you very much for your response. I've been calling it background noise, but perhaps we're saying the same thing. I mean, I really wan…
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